Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011634.1 Kokia drynarioides strain JFW-HI SEQ_126625, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124361
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:2188 original size:21 final size:21
Alignment explanation
Indices: 2159--2202 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2149 AATGTGTCTA
* *
2159 AATTATATTTTATATTTATTT
1 AATTATATTTTATAGTGATTT
*
2180 AATTCTATTTTATAGTGATTT
1 AATTATATTTTATAGTGATTT
2201 AA
1 AA
2203 ATATGTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
AATTATATTTTATAGTGATTT
Found at i:3621 original size:5 final size:5
Alignment explanation
Indices: 3611--3635 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3601 AAAAAACTTG
3611 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
3636 TAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3679 original size:19 final size:19
Alignment explanation
Indices: 3653--3701 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3643 TATTTTATAT
3653 TATG-ATTTAATATTTAAGA
1 TATGTATTTAATATTTAA-A
*
3672 TAT-TATTTATTATTTAAA
1 TATGTATTTAATATTTAAA
*
3690 TTTGTATTTAAT
1 TATGTATTTAAT
3702 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TATGTATTTAATATTTAAA
Found at i:4517 original size:15 final size:16
Alignment explanation
Indices: 4499--4528 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4489 CTTCCCTATT
4499 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
4514 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
4529 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:4521 original size:22 final size:22
Alignment explanation
Indices: 4494--4554 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
4484 TTCGACTTCC
4494 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
4516 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
4538 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
4555 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:4544 original size:21 final size:22
Alignment explanation
Indices: 4508--4554 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
4498 TTTCTATTTC
*
4508 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
4530 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
4551 TTTT
1 TTTT
4555 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:5106 original size:15 final size:15
Alignment explanation
Indices: 5086--5119 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5076 GGGTTAGATT
5086 TTTTGAG-TCAAATTA
1 TTTTGAGTTCAAA-TA
5101 TTTTGAGTTCAAATA
1 TTTTGAGTTCAAATA
5116 TTTT
1 TTTT
5120 TTATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTTGAGTTCAAATA
Found at i:26180 original size:10 final size:10
Alignment explanation
Indices: 26165--26201 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
26155 TATTATTCTA
26165 AATTTTTTTT
1 AATTTTTTTT
26175 AA--TTTTTT
1 AATTTTTTTT
26183 AATTTTTTTT
1 AATTTTTTTT
26193 AATTTTTTT
1 AATTTTTTT
26202 AGAACTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:26188 original size:18 final size:18
Alignment explanation
Indices: 26165--26200 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
26155 TATTATTCTA
26165 AATTTTTTTTAATTTTTT
1 AATTTTTTTTAATTTTTT
26183 AATTTTTTTTAATTTTTT
1 AATTTTTTTTAATTTTTT
26201 TAGAACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
AATTTTTTTTAATTTTTT
Found at i:35701 original size:21 final size:22
Alignment explanation
Indices: 35676--35719 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
35666 TTTAATTTTG
*
35676 TAGTTTATAT-TTTTTAAAATT
1 TAGTTAATATATTTTTAAAATT
* *
35697 TAGTTAATTTATTTTTCAAATT
1 TAGTTAATATATTTTTAAAATT
35719 T
1 T
35720 TAAAATTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TAGTTAATATATTTTTAAAATT
Found at i:35965 original size:31 final size:29
Alignment explanation
Indices: 35930--35999 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
35920 ACCCTAGAAT
*
35930 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
* * *
35961 TATACATGAACTTTGATTTTGTGTAATTT
1 TATACATGAACTATGATTTTGTGCAATTG
35990 TATACATGAA
1 TATACATGAA
36000 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:35993 original size:29 final size:30
Alignment explanation
Indices: 35929--36009 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
35919 AACCCTAGAA
* *
35929 TTATACATGAACTATGGTTTAATGTGCAATT
1 TTATACATGAACTTTGATTT-ATGTGCAATT
* *
35960 GTATACATGAACTTTGATTT-TGTGTAATT
1 TTATACATGAACTTTGATTTATGTGCAATT
*
35989 TTATACATGAAATTTTGATTT
1 TTATACATG-AACTTTGATTT
36010 GATCCAGTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 16 0.37
30 10 0.23
31 17 0.40
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (30 bp):
TTATACATGAACTTTGATTTATGTGCAATT
Found at i:36227 original size:29 final size:30
Alignment explanation
Indices: 36152--36240 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
36142 GATTAAATCA
* * * *
36152 AAATTAAAGTTTCAAGTATTTATTTGAACC
1 AAATTAAAGTTTCATGTATATAATTGCACC
* *
36182 ACAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAGTTTCATGTATATAATTGCACC
*
36213 AAATTAAAG-TTCATGTATACAATTGCAC
1 AAATTAAAGTTTCATGTATATAATTGCAC
36241 ATTAAATCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.35
30 8 0.16
31 24 0.49
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATATAATTGCACC
Found at i:40372 original size:3 final size:3
Alignment explanation
Indices: 40364--40389 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40354 ATACTTGTGA
40364 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
40390 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:41534 original size:34 final size:34
Alignment explanation
Indices: 41469--41534 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
41459 GGCCCGTCAT
*
41469 AAAAACATTAAAATAAATATTTCTCAATAAATTG
1 AAAAACATTAAAATAAATATTTATCAATAAATTG
*
41503 AAAATACATTAAAA-ATATATTTAT-AATTAAAT
1 AAAA-ACATTAAAATAAATATTTATCAA-TAAAT
41535 AACCTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.07
34 17 0.61
35 9 0.32
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (34 bp):
AAAAACATTAAAATAAATATTTATCAATAAATTG
Found at i:42291 original size:10 final size:10
Alignment explanation
Indices: 42276--42310 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
42266 GTAGAGTTTA
42276 ATAGTAAAAC
1 ATAGTAAAAC
*
42286 ATAGTAAAAA
1 ATAGTAAAAC
42296 ATCAGTAAAAC
1 AT-AGTAAAAC
42307 ATAG
1 ATAG
42311 ACTCAAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (10 bp):
ATAGTAAAAC
Found at i:43035 original size:2 final size:2
Alignment explanation
Indices: 43028--43055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43018 AATACAATAC
43028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43056 GTGAAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44499 original size:25 final size:23
Alignment explanation
Indices: 44410--44535 Score: 107
Period size: 23 Copynumber: 5.3 Consensus size: 23
44400 AGTACTTAAA
*
44410 AGAGGGCACATAAGTGCTGGATAAC
1 AGAGGGCACACAAGTGCT--ATAAC
*
44435 AGAGGGCACACAAAGTGCTA-ATC
1 AGAGGGCACAC-AAGTGCTATAAC
* *
44458 AAAGGACACACGAAGTGCTAATAAC
1 AGAGGGCACAC-AAGTGCT-ATAAC
*
44483 AGAGGGCACACACAGTGCTA-AAT
1 AGAGGGCACACA-AGTGCTATAAC
44506 AGAGGGCACGA-AACGTGCTA-AAC
1 AGAGGGCAC-ACAA-GTGCTATAAC
44529 AGAGGGC
1 AGAGGGC
44536 GCGCTAATGT
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
22 1 0.01
23 45 0.53
24 5 0.06
25 27 0.32
26 7 0.08
ACGTcount: A:0.40, C:0.20, G:0.29, T:0.12
Consensus pattern (23 bp):
AGAGGGCACACAAGTGCTATAAC
Found at i:44524 original size:48 final size:46
Alignment explanation
Indices: 44406--44535 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 46
44396 CCGAAGTACT
*
44406 TAAA-AGAGGGCACATAAGTGCTGGATAACAGAGGGCACACAAAGTGC
1 TAAATAGAGGGCACACAAGTGCT--ATAACAGAGGGCACACAAAGTGC
* * *
44453 T-AATCAAAGGACACACGAAGTGCTAATAACAGAGGGCACACACAGTGC
1 TAAAT-AGAGGGCACAC-AAGTGCT-ATAACAGAGGGCACACAAAGTGC
44501 TAAATAGAGGGCACGA-AACGTGCTA-AACAGAGGGC
1 TAAATAGAGGGCAC-ACAA-GTGCTATAACAGAGGGC
44536 GCGCTAATGT
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
46 12 0.17
47 4 0.06
48 43 0.61
49 11 0.16
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (46 bp):
TAAATAGAGGGCACACAAGTGCTATAACAGAGGGCACACAAAGTGC
Found at i:47788 original size:171 final size:173
Alignment explanation
Indices: 47502--47816 Score: 406
Period size: 171 Copynumber: 1.8 Consensus size: 173
47492 TAAATAAGAG
* * *
47502 AGTAAAATTTTGGAAGAAAAATATTCAAAAAAATTGAGGGGGGAATGAGTTTGGGGTAAATGGGG
1 AGTAAAATTTTGGAAGAAAAATATTAAAAAAAATTGAGGGGGAAATGAGTTTGGGGTAAATGAGG
*** * * *
47567 GTGGAATGAGAGGGGAGTAAAAGTTTTAAAGAAAAAGTAGGAAGGAGTAAAAGTTTTGAGG-GAA
66 GTGGAATGAGAGAAAAATAAAAGTTTTAAAGAAAAAGTAGGAAAGAGTAAAAATTTT-AGGAGAA
47631 AA-TAAAAA-ATTTTGAGGGTTTTTGGGGGAAGTAAATGGAAAC
130 AAGTAAAAATATTTTGAGGGTTTTTGGGGGAAGTAAATGGAAAC
* * * *
47673 AGTAAATTTTTGGAAGGAAAATATTAAAAAAAAATTG-GGGGGAAATGGGTTTGGGGTAGATTGA
1 AGTAAAATTTTGGAAGAAAAATATT-AAAAAAAATTGAGGGGGAAATGAGTTTGGGGTA-AATGA
* *** *
47737 GGGTGGGATGAGAGAAAAATAAAAGTTTTGGGGGAAAA-TAGGAAAGAGTAAAAATTTTAGGAGA
64 GGGTGGAATGAGAGAAAAATAAAAGTTTTAAAGAAAAAGTAGGAAAGAGTAAAAATTTTAGGAGA
47801 AAAGTAAAAATATTTT
129 AAAGTAAAAATATTTT
47817 AGGTTTGAGG
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
170 3 0.02
171 65 0.54
172 48 0.40
173 5 0.04
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (173 bp):
AGTAAAATTTTGGAAGAAAAATATTAAAAAAAATTGAGGGGGAAATGAGTTTGGGGTAAATGAGG
GTGGAATGAGAGAAAAATAAAAGTTTTAAAGAAAAAGTAGGAAAGAGTAAAAATTTTAGGAGAAA
AGTAAAAATATTTTGAGGGTTTTTGGGGGAAGTAAATGGAAAC
Found at i:48536 original size:31 final size:31
Alignment explanation
Indices: 48496--48566 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
48486 AAATAATCAT
* *
48496 TTTTATTTGCCTCTGATCATATTTTAGTCAC
1 TTTTGTTTGCCTCAGATCATATTTTAGTCAC
*
48527 TTTTGTTTGCCTCAGATCATATTTTAGTTAC
1 TTTTGTTTGCCTCAGATCATATTTTAGTCAC
*
48558 TTATGTTTG
1 TTTTGTTTG
48567 AAATGTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (31 bp):
TTTTGTTTGCCTCAGATCATATTTTAGTCAC
Found at i:49768 original size:25 final size:24
Alignment explanation
Indices: 49730--49779 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
49720 TTTAATTAAA
49730 TAAATATTAAAAATAA-ATATATTT
1 TAAATATTAAAAATAACA-ATATTT
*
49754 TAAATAATTATAAATAACAATATTT
1 TAAAT-ATTAAAAATAACAATATTT
49779 T
1 T
49780 TATCATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 17 0.74
26 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATATTAAAAATAACAATATTT
Found at i:71610 original size:24 final size:24
Alignment explanation
Indices: 71577--71627 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
71567 AGAAATAATC
*
71577 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
71601 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
71625 TTT
1 TTT
71628 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:71636 original size:24 final size:24
Alignment explanation
Indices: 71585--71639 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
71575 TCTTTCAGTT
*
71585 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * *
71609 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATC
71633 AAACTCT
1 AAACTCT
71640 TATCAATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:73541 original size:25 final size:23
Alignment explanation
Indices: 73500--73545 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
73490 CCAATTAGGG
73500 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
73523 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
73546 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:74583 original size:18 final size:19
Alignment explanation
Indices: 74562--74604 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
74552 CTTTAGCCAT
74562 TTTTATTATTT-ATTTTTA
1 TTTTATTATTTCATTTTTA
74580 TTTTATTATTTGCATTTTTA
1 TTTTATTATTT-CATTTTTA
*
74600 ATTTA
1 TTTTA
74605 ATTTTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTCATTTTTA
Found at i:74604 original size:31 final size:37
Alignment explanation
Indices: 74539--74610 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 37
74529 TTAGGAAAAC
74539 TTTATTTCTATTACTTTAGCCATTTTTATTATTT-ATT
1 TTTATTTCTATTACTTTAGCCATTTTTA-TATTTAATT
74576 TTTATTT-TATTA-TTT-G-CATTTTTA-ATTTAATT
1 TTTATTTCTATTACTTTAGCCATTTTTATATTTAATT
74608 TTT
1 TTT
74611 CTAATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
31 4 0.12
32 6 0.18
33 8 0.24
34 1 0.03
35 3 0.09
36 5 0.15
37 7 0.21
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (37 bp):
TTTATTTCTATTACTTTAGCCATTTTTATATTTAATT
Found at i:74615 original size:14 final size:13
Alignment explanation
Indices: 74594--74625 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
74584 ATTATTTGCA
74594 TTTTTAATTTAAT
1 TTTTTAATTTAAT
74607 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
74621 TTTTT
1 TTTTT
74626 CCCTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:80088 original size:10 final size:10
Alignment explanation
Indices: 80069--80111 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
80059 TTTTTTTTTT
*
80069 AAATTTAAAA
1 AAATTGAAAA
80079 AAATTGAAAAA
1 AAATTG-AAAA
80090 AAATTG-AAA
1 AAATTGAAAA
*
80099 AAATTCAAAA
1 AAATTGAAAA
80109 AAA
1 AAA
80112 AAATTTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 10 0.34
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATTGAAAA
Found at i:80091 original size:11 final size:11
Alignment explanation
Indices: 80075--80101 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
80065 TTTTAAATTT
80075 AAAAAAATTGA
1 AAAAAAATTGA
80086 AAAAAAATTGA
1 AAAAAAATTGA
80097 AAAAA
1 AAAAA
80102 TTCAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:80144 original size:12 final size:11
Alignment explanation
Indices: 80124--80183 Score: 68
Period size: 12 Copynumber: 5.2 Consensus size: 11
80114 ATTTAGTATA
80124 TTTATTTTCATT
1 TTTATTTT-ATT
*
80136 TTCATTTTCATT
1 TTTATTTT-ATT
80148 TTTAGTTTTA-T
1 TTTA-TTTTATT
80159 TTTATTTTATT
1 TTTATTTTATT
80170 TTTATTTTTATT
1 TTTA-TTTTATT
80182 TT
1 TT
80184 AATTATGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 5 0.12
11 10 0.23
12 24 0.56
13 4 0.09
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:80163 original size:5 final size:5
Alignment explanation
Indices: 80124--80184 Score: 59
Period size: 6 Copynumber: 10.8 Consensus size: 5
80114 ATTTAGTATA
80124 TTTAT TTTCAT TTTCAT TTTCATT TTTAGT TTTAT TTTAT TTTATT TTTATT
1 TTTAT TTT-AT TTT-AT TTT-A-T TTTA-T TTTAT TTTAT TTTA-T TTTA-T
80176 TTTAT TTTA
1 TTTAT TTTA
80185 ATTATGCAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
5 18 0.35
6 30 0.58
7 4 0.08
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:80963 original size:26 final size:26
Alignment explanation
Indices: 80933--80986 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
80923 TAAATTAATC
80933 CCTAGTGAGCCCCATTGAGCGTAACA
1 CCTAGTGAGCCCCATTGAGCGTAACA
80959 CCTAGTGAGCCCCATTGAGCGTAACA
1 CCTAGTGAGCCCCATTGAGCGTAACA
80985 CC
1 CC
80987 GTTCTATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.19
Consensus pattern (26 bp):
CCTAGTGAGCCCCATTGAGCGTAACA
Found at i:81186 original size:14 final size:15
Alignment explanation
Indices: 81163--81202 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
81153 GAAAAAAGTC
*
81163 GAAAAGAAAAATTGA
1 GAAAAAAAAAATTGA
81178 -AAAAAAAAAATTGA
1 GAAAAAAAAAATTGA
*
81192 GGAAAAAAAAA
1 GAAAAAAAAAA
81203 GACAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (15 bp):
GAAAAAAAAAATTGA
Found at i:81197 original size:15 final size:14
Alignment explanation
Indices: 81163--81202 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
81153 GAAAAAAGTC
81163 GAAAAGAAAAATTGA
1 GAAAA-AAAAATTGA
*
81178 AAAAAAAAAATTGA
1 GAAAAAAAAATTGA
81192 GGAAAAAAAAA
1 -GAAAAAAAAA
81203 GACAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (14 bp):
GAAAAAAAAATTGA
Found at i:82257 original size:25 final size:23
Alignment explanation
Indices: 82216--82261 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
82206 CCAATTAGGG
82216 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
82239 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
82262 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:83729 original size:24 final size:24
Alignment explanation
Indices: 83701--83763 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
83691 AGAAATAATC
*
83701 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
83725 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
83749 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
83764 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:88587 original size:17 final size:17
Alignment explanation
Indices: 88565--88598 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88555 AAAAAAATTC
*
88565 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
88582 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
88599 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:91561 original size:6 final size:6
Alignment explanation
Indices: 91550--91590 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
91540 TAGAATTAAA
*
91550 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
91591 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:91729 original size:22 final size:21
Alignment explanation
Indices: 91698--91738 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
91688 TTATTAAATA
*
91698 AATTCAAATTTAAGCATAATT
1 AATTCAAATTCAAGCATAATT
*
91719 AATTCTAAATTCAATCATAA
1 AATTC-AAATTCAAGCATAA
91739 ACTTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTCAAATTCAAGCATAATT
Found at i:94899 original size:21 final size:21
Alignment explanation
Indices: 94841--94904 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
94831 TTTAATTCAA
* *
94841 TTTTTTAATTTTATATTATTAT
1 TTTTTTAATTTTTTATAATT-T
* *
94863 TTTCTATAA-TTCTTATAATTT
1 TTT-TTTAATTTTTTATAATTT
94884 TTTTTTAATTTTTTATAATTT
1 TTTTTTAATTTTTTATAATTT
94905 GAATGGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
22 11 0.32
23 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTAATTTTTTATAATTT
Found at i:105405 original size:4 final size:4
Alignment explanation
Indices: 105396--105422 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
105386 AATAACAATA
105396 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
105423 ACCCACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:113096 original size:24 final size:24
Alignment explanation
Indices: 113051--113096 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
113041 CTATTTTTGC
** *
113051 GGATAAATATAATTATTTTATAAG
1 GGATAAATATAAAAATTATATAAG
113075 GGATAAATATAAAAATTATATA
1 GGATAAATATAAAAATTATATA
113097 TGAACTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (24 bp):
GGATAAATATAAAAATTATATAAG
Found at i:113777 original size:20 final size:21
Alignment explanation
Indices: 113754--113799 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
113744 ATTTTTATAT
*
113754 AATAATATTTTA-ATTTAAGA
1 AATAATATTTTATATTTAAAA
*
113774 AAT-ATATTTTATTTTTAAAA
1 AATAATATTTTATATTTAAAA
113794 AATAAT
1 AATAAT
113800 TATATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 12 0.55
21 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATAATATTTTATATTTAAAA
Found at i:116739 original size:6 final size:6
Alignment explanation
Indices: 116707--116801 Score: 88
Period size: 6 Copynumber: 16.0 Consensus size: 6
116697 CCCAATTCAT
** * *
116707 TTTAAA TTTATT TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
* * *
116754 TTTAAA TTT-AA TTTAAA TTTAAG TTTATA TTTGAA TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
116802 ATGAATAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 13 0.19
6 47 0.67
7 10 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:116749 original size:29 final size:29
Alignment explanation
Indices: 116707--116801 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 29
116697 CCCAATTCAT
116707 TTTAAATTTATTTTTAAATTT-ATTTTAAA
1 TTTAAATTTA-TTTTAAATTTAATTTTAAA
*
116736 TTTAAATTTATTTTAGAATTTAAATTT-AA
1 TTTAAATTTATTTTA-AATTTAATTTTAAA
* * *
116765 TTTAAATTTAAGTTTATATTTGAATTTAAAA
1 TTTAAATTT-ATTTTAAATTT-AATTTTAAA
116796 TTTAAA
1 TTTAAA
116802 ATGAATAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.09
29 30 0.54
30 13 0.23
31 8 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTAAATTTATTTTAAATTTAATTTTAAA
Found at i:116750 original size:11 final size:11
Alignment explanation
Indices: 116700--116739 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
116690 GCTGAAACCC
*
116700 AATTCATTTTA
1 AATTTATTTTA
116711 AATTTATTTTTA
1 AATTTA-TTTTA
116723 AATTTATTTTA
1 AATTTATTTTA
116734 AATTTA
1 AATTTA
116740 AATTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:116757 original size:18 final size:17
Alignment explanation
Indices: 116719--116799 Score: 108
Period size: 17 Copynumber: 4.6 Consensus size: 17
116709 TAAATTTATT
116719 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
116736 TTTAAATTTATTTTAGAA
1 TTTAAATTTATTTTA-AA
*
116754 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
* *
116771 TTTAAGTTTATATTTGAA
1 TTTAAATTTAT-TTTAAA
116789 TTTAAAATTTA
1 TTT-AAATTTA
116800 AAATGAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
17 26 0.46
18 24 0.43
19 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:116769 original size:35 final size:35
Alignment explanation
Indices: 116719--116800 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
116709 TAAATTTATT
*
116719 TTTAAATTTATTTTAAATTTAAATTTAT-TTTAGAA
1 TTTAAATTTAATTTAAATTTAAATTTATATTT-GAA
*
116754 TTTAAATTTAATTTAAATTTAAGTTTATATTTGAA
1 TTTAAATTTAATTTAAATTTAAATTTATATTTGAA
116789 TTTAAAATTTAA
1 TTT-AAATTTAA
116801 AATGAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 32 0.74
36 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTAAATTTAATTTAAATTTAAATTTATATTTGAA
Found at i:117554 original size:12 final size:13
Alignment explanation
Indices: 117535--117586 Score: 72
Period size: 12 Copynumber: 4.2 Consensus size: 13
117525 TTAGTCATAA
117535 TAATAAT-AATAT
1 TAATAATAAATAT
*
117547 TGATAATAAATAT
1 TAATAATAAATAT
*
117560 TAATAAT-AACAT
1 TAATAATAAATAT
117572 TAATAATAAATAT
1 TAATAATAAATAT
117585 TA
1 TA
117587 GCAATGAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 17 0.50
13 17 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:117606 original size:29 final size:25
Alignment explanation
Indices: 117535--117586 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
117525 TTAGTCATAA
* *
117535 TAATAATAATATTGATAATAAATAT
1 TAATAATAACATTAATAATAAATAT
117560 TAATAATAACATTAATAATAAATAT
1 TAATAATAACATTAATAATAAATAT
117585 TA
1 TA
117587 GCAATGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TAATAATAACATTAATAATAAATAT
Found at i:117641 original size:21 final size:21
Alignment explanation
Indices: 117599--117655 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
117589 AATGAATGAC
*
117599 ATTAATAAGTATTAACAGAAAT
1 ATTAATAA-TATTAACAAAAAT
**
117621 ATTAATAATATTAGTAAAAAT
1 ATTAATAATATTAACAAAAAT
*
117642 ATTAATAACATTAA
1 ATTAATAATATTAA
117656 TAATAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTAATAATATTAACAAAAAT
Found at i:117968 original size:24 final size:21
Alignment explanation
Indices: 117940--117997 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 21
117930 TTAAAAGTAT
117940 AAAAAAGGGAAAAGGATTTTCAA
1 AAAAAAGGGAAAAGGATTTT--A
**
117963 AGAAAAATCGAAAAGGATTTTA
1 A-AAAAAGGGAAAAGGATTTTA
117985 AAAAAAGGGAAAA
1 AAAAAAGGGAAAA
117998 AGAAAAGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 10 0.33
22 2 0.07
23 1 0.03
24 17 0.57
ACGTcount: A:0.60, C:0.03, G:0.21, T:0.16
Consensus pattern (21 bp):
AAAAAAGGGAAAAGGATTTTA
Found at i:118761 original size:30 final size:30
Alignment explanation
Indices: 118727--119046 Score: 188
Period size: 29 Copynumber: 10.9 Consensus size: 30
118717 CCCTAAAGGT
*** *
118727 CCTCGAAACTTTTGAAAATTATATTTTTGA
1 CCTCGAAACTTCCAAAAATTACATTTTTGA
*
118757 CCTCG-AACTTCCAAAAATTCCATTTTTGA
1 CCTCGAAACTTCCAAAAATTACATTTTTGA
118786 CCTCGAAACTTCCAAAAATTACA-TTTT-A
1 CCTCGAAACTTCCAAAAATTACATTTTTGA
* *
118814 CCCTC-AAATTTCCAAAAATTCCATTTTTGA
1 -CCTCGAAACTTCCAAAAATTACATTTTTGA
* * *** *
118844 CCCCAAAACTTTTGAAAAGTACATTTTT-A
1 CCTCGAAACTTCCAAAAATTACATTTTTGA
* **
118873 CC-CCAAACTAACAAAAATT-CTATTTTT-A
1 CCTCGAAACTTCCAAAAATTAC-ATTTTTGA
* *
118901 GCCCCGAAACTTCCAAAATTTACATTTTT-A
1 -CCTCGAAACTTCCAAAAATTACATTTTTGA
*
118931 CCCTCG-AACTTCCAAAAA-AATCA-TTTTGA
1 -CCTCGAAACTTCCAAAAATTA-CATTTTTGA
* * *
118960 CCCCTG-AACTTTCAAAAATCACCA-TTTT-A
1 CCTC-GAAACTTCCAAAAATTA-CATTTTTGA
* * *
118989 CCTCG-AA-TGTCCAAAAACTCCATTTTTTTA
1 CCTCGAAACT-TCCAAAAATTACA-TTTTTGA
**
119019 CCTCGAAACTTTTAAAAATTACCATTTT
1 CCTCGAAACTTCCAAAAATTA-CATTTT
119047 ACCCCCGAAT
Statistics
Matches: 228, Mismatches: 42, Indels: 39
0.74 0.14 0.13
Matches are distributed among these distances:
27 4 0.02
28 53 0.23
29 78 0.34
30 76 0.33
31 14 0.06
32 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
CCTCGAAACTTCCAAAAATTACATTTTTGA
Found at i:118845 original size:58 final size:58
Alignment explanation
Indices: 118730--119194 Score: 293
Period size: 58 Copynumber: 7.9 Consensus size: 58
118720 TAAAGGTCCT
** * * *
118730 CGAAACTTTTGAAAATTATATTTTTGA-CCTCGAACTTCCAAAAATTCCATTTTTGACCT
1 CGAAACTTTCAAAAATTACA-TTTT-ACCCTCGAATTTCCAAAAATTCCATTTTTGACCC
* *
118789 CGAAACTTCCAAAAATTACATTTTACCCTCAAATTTCCAAAAATTCCATTTTTGACCC
1 CGAAACTTTCAAAAATTACATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCC
* ** * * * ** *
118847 CAAAACTTTTGAAAAGTACATTTTTACCC-CAAACTAACAAAAATTCTATTTTT-AGCCC
1 CGAAACTTTCAAAAATTACA-TTTTACCCTCGAATTTCCAAAAATTCCATTTTTGA-CCC
* * * *
118905 CGAAACTTCCAAAATTTACATTTTTACCCTCGAACTTCCAAAAAAAT-CA-TTTTGACCC
1 CGAAACTTTCAAAAATTACA-TTTTACCCTCGAATTTCC-AAAAATTCCATTTTTGACCC
* * * * *
118963 CTG-AACTTTCAAAAATCACCATTTTA-CCTCGAATGTCCAAAAACTCCATTTTTTTACCT
1 C-GAAACTTTCAAAAATTA-CATTTTACCCTCGAATTTCCAAAAATTCCA-TTTTTGACCC
* * * * *
119022 CGAAACTTTTAAAAATTACCATTTTACCCCCGAATGTT-CAAAAATTCCGTTTTTGATCT
1 CGAAACTTTCAAAAATTA-CATTTTACCCTCGAAT-TTCCAAAAATTCCATTTTTGACCC
*** * * * * * * * *
119081 CGATTTTTTCTAAAAATTACCGTTTTATCATTGAATAT-CTAAAATTTCATTTTTAACCC
1 CGAAACTTTC-AAAAATTA-CATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCC
* * * * *
119140 C-AAATTTTCCCAAAATTACCATTTTACCCCTCGAGTATCCAAAAAGTCTCATTTT
1 CGAAACTTT-CAAAAATTA-CATTTTA-CCCTCGAATTTCCAAAAATTC-CATTTT
119195 CAATGCCGAT
Statistics
Matches: 317, Mismatches: 70, Indels: 36
0.75 0.17 0.09
Matches are distributed among these distances:
56 6 0.02
57 14 0.04
58 139 0.44
59 103 0.32
60 48 0.15
61 7 0.02
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (58 bp):
CGAAACTTTCAAAAATTACATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCC
Found at i:122192 original size:8 final size:8
Alignment explanation
Indices: 122179--122209 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
122169 TACAAACTTA
122179 AAAAATTC
1 AAAAATTC
*
122187 AAAAATTT
1 AAAAATTC
122195 AAAAATTC
1 AAAAATTC
122203 AAAAATT
1 AAAAATT
122210 TTAAAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAATTC
Found at i:122200 original size:16 final size:17
Alignment explanation
Indices: 122179--122215 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
122169 TACAAACTTA
122179 AAAAATTCAAAAA-TTT
1 AAAAATTCAAAAATTTT
122195 AAAAATTCAAAAATTTT
1 AAAAATTCAAAAATTTT
122212 AAAA
1 AAAA
122216 CTTATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATTCAAAAATTTT
Done.